Hiding ontologies under the carpet

Frederic Bastian – Bgee teamOntoSIB - August 2013

© 2013 SIB

Big players of Internet never exhibit ontologies

Amazon:

© 2013 SIB

Big players of Internet never exhibit ontologies

Google Knowledge Graph:

© 2013 SIB

Big players of Internet never exhibit ontologies

Google Knowledge Graph:

© 2013 SIB

Big players of Internet never exhibit ontologies

Facebook Open Graph:

© 2013 SIB

Big players of Internet never exhibit ontologies

Facebook Open Graph:

© 2013 SIB

Meanwhile… Bgee is ontology-centric

Expression of mouse Hoxa5

© 2013 SIB

Meanwhile… Bgee is ontology-centric

Expression of mouse Hoxa5

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But lists are not usable…

Expression of mouse Hoxa5

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Neither are tables

Expression of mouse Hoxa5

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Solutions are…

On the analytical side: - identify the most pertinent biological signal

On the visualization side: - display the most pertinent information (e.g., remove

redundancy)- guide users to the information they look for

© 2013 SIB

Solutions are…

On the analytical side: - identify the most pertinent biological signal

On the visualization side: - display the most pertinent information (e.g., remove

redundancy)- guide users to the information they look for

But an ontology-centric display is terrible at guidance and pertinence.

© 2013 SIB

The solution adopted by neXtProt

Revamp the ontologies to make the organization clearer, and the hierarchy simpler.

© 2013 SIB

Bgee needs a different approach

- Bgee includes several species; revamping ontologies would be too time-consuming.

- Bgee includes in situ hybridizations with great granularity; we don’t want to loose it.

- Things are getting even worse with the use of the Uberon ontology.

We are now trying the approach of completely hiding the ontologies to the users!

© 2013 SIB

Solution 1

Summarize information on the fly:

Find by walking the ontology from the root the x most general terms

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Solution 1

1. Start walk from the root

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Solution 1

1. Start walk from the root

2. Walk 1st level

2 terms identified

© 2013 SIB

Solution 1

1. Start walk from the root

2. Walk 1st level

3a. Walk 2nd level 1st term

2 terms identified

© 2013 SIB

Solution 1

1. Start walk from the root

2. Walk 1st level

3a. Walk 2nd level 1st term

3b. Walk 2nd level 2nd term

2 terms identified

© 2013 SIB

Solution 1

1. Start walk from the root

2. Walk 1st level

3a. Walk 2nd level 1st term

3b. Walk 2nd level 2nd term

4a. Walk 3rd level 1st term

4 terms identified

© 2013 SIB

Solution 1

1. Start walk from the root

2. Walk 1st level

3a. Walk 2nd level 1st term

3b. Walk 2nd level 2nd term

4a. Walk 3rd level 1st term

4b. Walk 3rd level 2nd term

11 terms identified

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Solution 1

EMAPA:16060 cavities and their linings

EMAPA:16072 primitive streak

EMAPA:16097 mesenchyme

EMAPA:16103 organ system

EMAPA:16405 limb

EMAPA:16748 tail

EMAPA:17213 skeleton

EMAPA:17743 vertebral axis muscle system

MA:0000003 organ system

MA:0002405 postnatal mouse

MA:0002433 anatomic region

11 terms identified

© 2013 SIB

Solution 1

EMAPA:16060 cavities and their linings

EMAPA:16072 primitive streak

EMAPA:16097 mesenchyme

EMAPA:16103 organ system

EMAPA:16405 limb

EMAPA:16748 tail

EMAPA:17213 skeleton

EMAPA:17743 vertebral axis muscle system

MA:0000003 organ system

MA:0002405 postnatal mouse

MA:0002433 anatomic region

Uberon includes “subsets” that would allow to filter meaningless terms

© 2013 SIB

Solution 2

Find most precise and independent terms:

Walk the ontology from the leaves to the root.

Data found in a term will prevent its ancestors from being display (redundancy), but not its siblings (independency).

© 2013 SIB

Solution 2

1. Start the walk from the leaves

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Solution 2

1. Start the walk from the leaves

2. Remove ancestors

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Solution 2

Limb example:

EMAPA:17459 footplate

EMAPA:17428 handplate

EMAPA:17713 humerus cartilage condensation

EMAPA:16779 hindlimb bud

EMAPA:16406 forelimb bud

- Visualization tool should allow to easily get information about ancestors of selected terms.

- This solution could still lead to an unorganized list of many terms

© 2013 SIB

Solution 3

Display most precise and independent terms, organized by most general terms

© 2013 SIB

Solution 3

Example: general terms

EMAPA:16405 limb

EMAPA:16748 tail

EMAPA:17213 skeleton

© 2013 SIB

Solution 3

Example: general terms + precise and independent terms

EMAPA:16405 limbEMAPA:17459 footplate

EMAPA:17428 handplate

EMAPA:17713 humerus cartilage condensation

EMAPA:16779 hindlimb bud

EMAPA:16406 forelimb bud

EMAPA:16748 tailEMAPA:16752 unsegmented mesenchyme

EMAPA:17213 skeleton EMAPA:18344 sternum

EMAPA:19387 S1

EMAPA:19388 S2

EMAPA:19364 S3

EMAPA:19365 S4

EMAPA:18010 rib

© 2013 SIB

OWLGraphManipulator allows to perform:

• enhanced relation reductions• class removal and relation propagation• relation mapping to parent• relation filtering or removal• subgraph filtering or removal• relation removal to subset if non orphan• combination of these methods for generating basic

ontologies

Used to simplify the Uberon ontology.

Owltools enhancement – OWLGraphManipulator

© 2013 SIB

Use of OWLGraphManipulator on Uberon:

• From the global version, keep only relevant species. • Clear relations to upper_level (obscure) terms• Remove subgraphs of obscure terms, keeping shared

classes• keep only is_a, part_of, develops_from, and sub-relations• Simplify graph structure over is_a/part_of

Uberon tweaking

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Development of an ontology to capture confidence in an annotation, following the Biocuration 2012 meeting.

http://wiki.isb-sib.ch/biocuration/Confidence_information_draft

Quality codes

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We annotate homology using Uberon, by providing for each annotation:

• Uberon ID UBERON:0003126 trachea

• NCBI taxon ID 32523 Tetrapoda

• HOM ID HOM:0000007 historical homology

• Evidence Code ID ECO:0000060 positional similarity evidence

• Confidence Code ID CONF:0000003 High confidence

• References ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF,

Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.591-592 »

Homology annotation

© 2013 SIB

Conclusion

Some big players on internet make an intensive use of ontologies (Amazon, Google, Facebook, …)

They invest a lot in usability and user-friendliness. What we can learn from them is:

They never, ever, display ontologies as such

© 2013 SIB

Conclusion

In bioinformatics, we have much more information to capture in ontologies.

But the lack of usability prevent biologists to access this knowledge.

It is now time to invest more in usability.

We hope that our approach will make easier the use of ontologies to analyse gene expression data.

Thank You

Marta RosikiewiczSébastien Moretti

Anne Niknejad

Mathieu Seppey

Marc Robinson-Rechavi